---
title: "SADBank - A database of standard area diagrams"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    theme: 
      version: 4
      navbar-bg: "#1E4571"
      bootswatch: yeti
    social: menu
    source: embed
      
---

```{r setup, include=FALSE}
library(tidyverse)
library(flexdashboard)
library(janitor)
library(readxl)
library(cowplot)
library(see)
library(plotly)
library(gsheet)
library(googlesheets4)
dat_sad <- gsheet2tbl("https://docs.google.com/spreadsheets/d/1oBa_OIko04157D0-Z0tV7dN8BJxq9fAjEfbOkoSKy5s/edit?usp=sharing")
attach(dat_sad)
dat_sad$citation <- paste(author, pub_year)
dat_sad$study_diag <- with(dat_sad, interaction(study, diag_id))
dat_sad$citation_diag <- with(dat_sad, interaction(citation, diag_id))
detach(dat_sad)
# aggregate by individual studies
dat_sad <- group_by(dat_sad, citation_diag)
dat_sad1 <- filter(dat_sad, row_number()==1 )
dat_sad2 <- ungroup(dat_sad1)
table1 <- select(dat_sad2, pub_year, crop,  pathogen, pathogen_group, organ,  citation, link1, link, link2)
table1 <- arrange(table1, -pub_year)
table1 <- unite(table1, weblink, link1, link, link2, sep = "")

```

```{r include=FALSE, layout="l-page"}
library(crosstalk)
sd <- SharedData$new(table1)
```

Inputs {.sidebar}
-------------------------------------

**Filters**

```{r}
filter_slider("year", "Publication year", sd, ~pub_year, round = TRUE)
filter_select("cropname", "Crop name", sd, ~crop)
filter_select("pathogen", "Pathogen species name", sd, ~pathogen)

```

**SADBank** is a curated collection of studies on Standard Area Diagram sets (SADs), a pictorial representations of disease symptoms and/or signs in a plant organ where each diagram depicts a percent diseased area. They are designed in a wide range of styles and are used as tools to use during or prior to visual assessments of disease severity to “calibrate” a rater’s eye and improve accuracy, precision and reliability of the estimates.


Author and maintainer: Emerson M. Del Ponte, Ignácio Cazón
Collaborators: Kaíque S. Alves, Sheila M. Andrade, Clive H. Bock, Sami J. Michereff, Sarah J. Pethybridge


Row
--------------

### Number of SADs

```{r}
articles <- nrow(table1)
valueBox(articles,  icon = "fa-ruler")
```

### Number of Hosts

```{r}
hosts <- table1 %>% 
  tabyl(crop) %>% 
  count()
valueBox(hosts,  icon = "fa-pagelines")
```

### Number of Pathogens

```{r}
pathogen <- table1 %>% 
  tabyl(pathogen) %>% 
  count()

valueBox(pathogen,  icon = "fa-leaf")
```




Row {data-height=650}
-------------------------------------





### List of articles

```{r}
library(DT)
datatable(sd, 
          escape = FALSE,
          class = 'cell-border stripe',
        rownames = FALSE, colnames = c('Year','Crop', 'Pathogen',  'Pathogen group', 'Organ', 'citation', 'Ref'), 
          options = list(
  pageLength = 12,
  fontSize = 9,
  lengthMenu = c(25, 50, 100, 500 )
))%>%
formatStyle(
  c('pub_year', 'crop',  'pathogen', 'pathogen_group', 'organ',   'citation', 'weblink'),
  fontSize = '100%')

```